The location of Isaac Jones's birth is open to speculation. On the 1871 and 1881 census returns he states it is Liverpool and on the 1861 it has Amlwch. The Family Trees for him on Ancestry show he was born in elsewhere in Anglesey. At present it isn't possible to find any baptism for him which is certain. There are baptisms on Freereg for Isaac Jones baptised Holyhead, St Cybi, on 30/07/1810, son of Richard and Elizabeth Jones. Also, 29/03/1813, baptised Isaac Jones, son of Hugh Jones and Elizabeth Perry at Llanfair Mathafarn Eithaf.
The illegitimate daughter of Miriam Owen was born in Liverpool in 1860, so there was a connection to there.
I have found Ellen Jones in the 1911 census, she is still living at 2 Water St, Hirael, Bangor. I noticed that she lived there whilst married to Owen Richards. They are there in the 1871 census with a son, William, age 1 and daughter, Margaret, age 3.
I am a bit intrigued by the occupation of Edward Jones shown as Naturalist in the 1881 census.
I wonder if Edward Jones is in Dwygyfylchi in the 1841 census. The Household is:
Richard Jones, age 20, Smith, born in county.
Elizabeth Jones, age 25, born in county.
Peter Jones, age 3, born in county.
Edward Jones, age 7 months, born in county.
The location looks to be Penman Isa.
This appears to be the same family living in Holyhead in the 1851 census. Richard Jones was age 35 and a Blacksmith in that census. As the year of birth was rounded up, or down, to the nearest 5 years in the 1841, he could have been older than 20 then. His wife, Elizabeth, was age 39 in 1851. The age of Elizabeth is older than Richard, the same as the 1841. They also have a son, Peter, age 14 in 1851.
There is a baptism for Richard Jones in St Tudno, Llandudno, on 11 May 1817, son of Peter and Elizabeth Jones. I think this is the person you suspect of being Edward's father.
Edward would have left home by 1861 but his family should be around. This search will be for another day!
There is a family in Llandudno with a son named Edward Jones, and he is aged 1 in the 1841 census. This is headed by Robert Jones age 25, Copper Miner, not born in county. They are living in Price St.
Helig.